Development of nuclear and plastid SNP markers for genetic studies of Dipteryx tree species in Amazonia

Honorio Coronado, Euridice, N.; Blanc-Jolivet, Céline; Mader, Malte; Garcia-Davila, Carmen, R.; Sebbenn, Alexandre, Magno; Meyer-Sand, Barbara, R., V.; Paredes-Villanueva, Kathelyn; Tysklind, Niklas; Troispoux, Valérie; Massot, Marie; Degen, Bernd

doi:10.1007/s12686-019-01081-3

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Development of nuclear and plastid SNP markers for genetic studies of Dipteryx tree species in Amazonia

Honorio Coronado, Euridice N.; Blanc-Jolivet, Céline ; Mader, Malte ; Garcia-Davila, Carmen R.; Sebbenn, Alexandre Magno ; Meyer-Sand, Barbara R. V.; Paredes-Villanueva, Kathelyn; Tysklind, Niklas; Troispoux, Valérie; Massot, Marie; Degen, Bernd

We developed nuclear and plastid single nucleotide polymorphism (SNP) and insertion/deletion (INDEL) markers for Dipteryx species using a combination of restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing. Of the total 315 loci genotyped using a MassARRAY platform, 292 loci were variable and polymorphic among the 73 sampled individuals from French Guiana, Brasil, Peru, and Bolivia. A final set of 56 nuclear SNPs, 26 chloroplast SNPs, 2 chloroplast INDELs, and 32 mitochondrial SNPs identifying significant population structure was developed. This set of loci will be useful for studies on population genetics of Dipteryx species in Amazonia.